[English] 日本語
Yorodumi
- PDB-2pn2: CRYSTAL STRUCTURE OF A PUTATIVE OSMOTIC STRESS INDUCED AND DETOXI... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2pn2
TitleCRYSTAL STRUCTURE OF A PUTATIVE OSMOTIC STRESS INDUCED AND DETOXIFICATION RESPONSE PROTEIN (PSYC_0566) FROM PSYCHROBACTER ARCTICUS 273-4 AT 2.15 A RESOLUTION
ComponentsUncharacterized protein
KeywordsSIGNALING PROTEIN / PUTATIVE OSMOTIC STRESS INDUCED AND DETOXIFICATION RESPONSE PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homologyOsmC/Ohr family / OsmC/Ohr superfamily / OsmC-like protein / K homology (KH) domain / GMP Synthetase; Chain A, domain 3 / K homology domain-like, alpha/beta / 2-Layer Sandwich / Alpha Beta / Osmotically inducible protein OsmC
Function and homology information
Biological speciesPsychrobacter arcticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of uncharacterized protein (YP_263861.1) from Psychrobacter arcticus 273-4 at 2.15 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAINS. ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAINS. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6294
Polymers17,4621
Non-polymers1673
Water1,18966
1
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2588
Polymers34,9242
Non-polymers3346
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area6800 Å2
ΔGint-110 kcal/mol
Surface area12740 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)47.243, 57.390, 103.398
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-196-

HOH

DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

-
Components

#1: Protein Uncharacterized protein


Mass: 17462.006 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psychrobacter arcticus (bacteria) / Strain: 273-4 / Gene: YP_263861.1, Psyc_0566 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q4FU81
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.69 %
Description: ICE RINGS WERE EXCLUDED DURING DATA INTEGRATION BY MOSFLM
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.43
Details: NANODROP, 0.2M Ammonium sulfate, 30.5% PEG MME 2000, 0.1M Sodium acetate pH 4.43, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162, 0.97939, 0.97922
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 1, 2007 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979391
30.979221
ReflectionResolution: 1.95→36.466 Å / Num. obs: 8085 / % possible obs: 76.3 % / Redundancy: 4 % / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 11.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.95-2.063.90.2223.234718830.22258.3
2.06-2.1840.1165.8414510310.11671.5
2.18-2.333.90.1036.424916320.10346.5
2.33-2.5240.0778.2505212560.07799.8
2.52-2.7640.05810.732808230.05869.8
2.76-3.0840.04313.7427510580.04399.7
3.08-3.5640.03913.432458110.03986.4
3.56-4.363.90.03317.723496010.03374.9
4.36-6.173.90.03118.225016460.03199.5
6.17-36.473.50.0230.711903440.0293.4

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0019refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.95→36.466 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / SU B: 7.676 / SU ML: 0.111 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.252 / ESU R Free: 0.201
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. CL AND SO4 IONS FROM THE CRYSTALLIZATION SOLUTION ARE MODELED. 4. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 5. RESIDUES 132-136 ARE DISORDERED AND ARE NOT MODELED. 6. THE RESOLUTION SHELLS CORRESPONDING TO ICE RINGS WERE REMOVED DURING THE INTEGRATION OF THE DATA. THIS RESULTED IN LOWER COMPLETENESS. 7. THE NOMINAL RESOLUTION IS 2.15 A WITH 1570 OBSERVED REFLECTIONS BETWEEN 2.15-1.95 (59.8% COMPLETE FOR THIS SHELL) INCLUDED IN THE REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.242 393 4.9 %RANDOM
Rwork0.195 ---
all0.197 ---
obs0.197 8065 76.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.711 Å2
Baniso -1Baniso -2Baniso -3
1--1.32 Å20 Å20 Å2
2---2.55 Å20 Å2
3---3.87 Å2
Refinement stepCycle: LAST / Resolution: 1.95→36.466 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1030 0 7 66 1103
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221076
X-RAY DIFFRACTIONr_bond_other_d0.0030.02689
X-RAY DIFFRACTIONr_angle_refined_deg1.6311.9591471
X-RAY DIFFRACTIONr_angle_other_deg1.3731708
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9995144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.41824.63441
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.35815184
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.428155
X-RAY DIFFRACTIONr_chiral_restr0.0990.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021189
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02200
X-RAY DIFFRACTIONr_nbd_refined0.1820.2171
X-RAY DIFFRACTIONr_nbd_other0.1420.2630
X-RAY DIFFRACTIONr_nbtor_refined0.1440.2551
X-RAY DIFFRACTIONr_nbtor_other0.0690.2527
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1030.255
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0970.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1370.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0930.217
X-RAY DIFFRACTIONr_mcbond_it1.6473729
X-RAY DIFFRACTIONr_mcbond_other0.393278
X-RAY DIFFRACTIONr_mcangle_it2.57651136
X-RAY DIFFRACTIONr_scbond_it4.3318397
X-RAY DIFFRACTIONr_scangle_it6.26911331
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 44 -
Rwork0.25 697 -
obs-741 98.54 %
Refinement TLS params.Method: refined / Origin x: 5.368 Å / Origin y: -1.96 Å / Origin z: 23.018 Å
111213212223313233
T-0.1563 Å20.0143 Å2-0.0533 Å2--0.1916 Å2-0.0237 Å2---0.2499 Å2
L3.0018 °20.7331 °2-0.8553 °2-2.0934 °2-0.02 °2--2.6933 °2
S-0.0716 Å °0.0562 Å °-0.177 Å °-0.0435 Å °0.1909 Å °-0.1399 Å °0.066 Å °0.1565 Å °-0.1192 Å °
Refinement TLS groupSelection: ALL

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more